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- PDB-3erj: Crystal structure of the peptidyl-tRNA hydrolase AF2095 from Arch... -

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Basic information

Entry
Database: PDB / ID: 3erj
TitleCrystal structure of the peptidyl-tRNA hydrolase AF2095 from Archaeglobus fulgidis. Northeast Structural Genomics Consortium target GR4
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / alpha-beta / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Cytoplasm
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / translation / cytosol
Similarity search - Function
Peptidyl-tRNA hydrolase, archaea / Peptidyl-tRNA hydrolase, PTH2 / Peptidyl-tRNA hydrolase PTH2 / Bit1 / Bit1 / Peptidyl-tRNA hydrolase II domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsForouhar, F. / Su, M. / Seetharaman, J. / Conover, K. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Cooper, B. / Baran, M.C. ...Forouhar, F. / Su, M. / Seetharaman, J. / Conover, K. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Cooper, B. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the peptidyl-tRNA hydrolase AF2095 from Archaeglobus fulgidis. Northeast Structural Genomics Consortium target GR4
Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Conover, K. / Janjua, H. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Cooper, B. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
B: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)27,1582
Polymers27,1582
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-18 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.903, 46.925, 105.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 13578.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF2095, AF_2095, pth / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O28185, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM Tris (pH 8), 20% PEG3350, 200 mM NaCl, and 0.5% w/v polyvinylpyrrolidone K15 , VAPOR ...Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM Tris (pH 8), 20% PEG3350, 200 mM NaCl, and 0.5% w/v polyvinylpyrrolidone K15 , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97877 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 30, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97877 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 38938 / Num. obs: 38783 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.043 / Net I/σ(I): 34.46
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 4.45 / Num. unique all: 3798 / Rsym value: 0.233 / % possible all: 97.5

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Processing

SoftwareName: CNS / Version: 1.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RLK

1rlk


Resolution: 1.8→19.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 114421.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1768 5 %RANDOM
Rwork0.195 ---
all0.197 38933 --
obs0.195 35196 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.7469 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.08 Å20 Å20 Å2
2--7.83 Å20 Å2
3----3.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 0 152 1886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.26 146 5.5 %
Rwork0.199 2529 -
obs-2529 68.9 %

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